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- PDB-4wbt: Crystal structure of histidinol-phosphate aminotransferase from S... -

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Basic information

Entry
Database: PDB / ID: 4wbt
TitleCrystal structure of histidinol-phosphate aminotransferase from Sinorhizobium meliloti in complex with pyridoxal-5'-phosphate
ComponentsProbable histidinol-phosphate aminotransferase
KeywordsTRANSFERASE / Histidinol-phosphate aminotransferase / Pyridoxal-5'-phosphate / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


histidinol-phosphate transaminase / histidinol-phosphate transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PYRIDOXAL-5'-PHOSPHATE / Probable histidinol-phosphate aminotransferase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsShabalin, I.G. / Bacal, P. / Kowalska, A.K. / Cooper, D.R. / Stead, M. / Hammonds, J. / Ahmed, M. / Hillerich, B.S. / Bonanno, J. / Seidel, R. ...Shabalin, I.G. / Bacal, P. / Kowalska, A.K. / Cooper, D.R. / Stead, M. / Hammonds, J. / Ahmed, M. / Hillerich, B.S. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: to be published
Title: Crystal structure of histidinol-phosphate aminotransferase from Sinorhizobium meliloti in complex with pyridoxal-5'-phosphate
Authors: Shabalin, I.G. / Cooper, D.R. / Minor, W.
History
DepositionSep 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 13, 2022Group: Database references / Refinement description / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / refine_hist
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.4Dec 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable histidinol-phosphate aminotransferase
B: Probable histidinol-phosphate aminotransferase
C: Probable histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,54513
Polymers120,7833
Non-polymers1,76310
Water18,1591008
1
A: Probable histidinol-phosphate aminotransferase
hetero molecules

C: Probable histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7819
Polymers80,5222
Non-polymers1,2597
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area9500 Å2
ΔGint-15 kcal/mol
Surface area25290 Å2
MethodPISA
2
B: Probable histidinol-phosphate aminotransferase
hetero molecules

B: Probable histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5298
Polymers80,5222
Non-polymers1,0076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area8400 Å2
ΔGint-30 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.055, 64.322, 137.048
Angle α, β, γ (deg.)90.000, 93.240, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-565-

HOH

21A-601-

HOH

31A-631-

HOH

41B-593-

HOH

51B-594-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA0 - 3703 - 373
21LEULEUBB0 - 3703 - 373
12LEULEUAA0 - 3703 - 373
22LEULEUCC0 - 3703 - 373
13ALAALABB0 - 3713 - 374
23ALAALACC0 - 3713 - 374

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Probable histidinol-phosphate aminotransferase


Mass: 40260.895 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (bacteria) / Strain: 1021 / Gene: hisC4, R01049, SMc02393 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: Q92R63, histidinol-phosphate transaminase

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Non-polymers , 6 types, 1018 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1008 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 ul of 17.6 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG-I condition #94 (0.1 M HEPES:NaOH pH 7.5, ...Details: 0.2 ul of 17.6 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG-I condition #94 (0.1 M HEPES:NaOH pH 7.5, 25% (w/v) PEG 3350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 20, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 150339 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.053 / Rrim(I) all: 0.085 / Χ2: 1.293 / Net I/av σ(I): 22.1 / Net I/σ(I): 9 / Num. measured all: 690744
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.634.20.5742.38137850.6790.3870.6250.63198.6
1.63-1.662.20.446142960.720.3580.5740.6396.2
1.66-1.692.30.384143680.7580.310.4950.64497.5
1.69-1.722.30.333144240.8040.270.430.65898.2
1.72-1.762.30.284145580.8490.230.3670.67198.7
1.76-1.82.30.241146980.8850.1960.3120.69199.2
1.8-1.852.30.202147130.9130.1650.2620.72299.6
1.85-1.92.30.174147490.9320.1420.2260.76299.8
1.9-1.952.40.142148110.9570.1150.1830.81599.9
1.95-2.022.40.116147580.970.0930.1490.869100
2.02-2.092.40.1148100.9780.080.1290.955100
2.09-2.172.40.083147460.9840.0670.1071.048100
2.17-2.272.40.078147520.9850.0620.11.143100
2.27-2.392.40.067147860.9890.0540.0861.287100
2.39-2.542.40.063147960.990.050.0811.461100
2.54-2.742.40.06147400.9910.0470.0761.744100
2.74-3.012.40.055147300.9920.0440.0712.16399.9
3.01-3.452.40.048147960.9940.0380.0622.59199.8
3.45-4.342.40.042147090.9950.0330.0542.96599.4
4.34-502.40.037146450.9960.030.0482.82599.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-3000data collection
HKL-3000phasing
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.1593 / WRfactor Rwork: 0.1413 / FOM work R set: 0.8956 / SU B: 2.94 / SU ML: 0.051 / SU R Cruickshank DPI: 0.0725 / SU Rfree: 0.0693 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1634 7537 5 %RANDOM
Rwork0.1461 142544 --
obs0.1469 142544 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.36 Å2 / Biso mean: 21.303 Å2 / Biso min: 8.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-0 Å2-0.21 Å2
2--0.57 Å2-0 Å2
3----0.78 Å2
Refinement stepCycle: final / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8214 0 96 1024 9334
Biso mean--28.2 34.27 -
Num. residues----1104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198862
X-RAY DIFFRACTIONr_bond_other_d0.0060.028619
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.98812143
X-RAY DIFFRACTIONr_angle_other_deg1.225319817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84551209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.38123.125368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42151316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2461577
X-RAY DIFFRACTIONr_chiral_restr0.0810.21393
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110176
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021979
X-RAY DIFFRACTIONr_mcbond_it0.7690.9324522
X-RAY DIFFRACTIONr_mcbond_other0.7680.9324521
X-RAY DIFFRACTIONr_mcangle_it1.2761.3935670
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A21919
12B21919
21A21835
22C21835
31B22071
32C22071
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 539 -
Rwork0.239 10373 -
all-10912 -
obs--98.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.53341.9993-2.83223.1531-2.54748.84220.06490.12190.2271-0.00580.07060.2674-0.7487-0.5011-0.13550.17830.0487-0.10370.0988-0.00780.157730.00120.59105.877
29.2772-1.47243.27583.77292.508514.4399-0.1596-0.35680.1796-0.08260.0115-0.1393-0.1889-0.61260.14810.07030.0533-0.01430.1179-0.01150.01530.55216.41198.87
30.526-0.52260.32790.742-0.20790.78610.054-0.057-0.0614-0.09470.01010.03220.1245-0.0433-0.06410.0419-0.0079-0.00170.06190.00820.018611.186-2.15484.143
40.62470.03770.11241.561-0.35330.826-0.0299-0.01410.06840.0274-0.0069-0.0375-0.12360.0990.03690.0479-0.00940.00490.06780.0060.052423.16219.50680.083
53.12530.41220.19080.9004-0.28641.4337-0.02320.09190.1527-0.0694-0.0237-0.0673-0.14450.08180.04680.1029-0.01320.00840.05690.02510.091321.40322.92671.23
61.27140.0796-0.03480.4774-0.19311.0073-0.01150.026-0.0414-0.0916-0.0219-0.06720.06750.08320.03350.05530.01310.0210.070.00140.050921.3959.34175.582
72.1186-1.4761.15181.3935-0.82681.50190.0822-0.0185-0.1034-0.1133-0.03140.07620.1664-0.0248-0.05080.0597-0.0031-0.00630.09080.00180.04656.711.3476.555
82.2512-1.0431-0.3662.14630.6372.60860.0011-0.04080.3834-0.0653-0.04780.02-0.4429-0.28730.04660.08910.0702-0.01940.0835-0.02080.0914-2.15326.26579.327
97.7242-1.262-0.44915.6906-0.47575.4369-0.1214-0.31340.53960.1990.025-0.1246-0.4485-0.11890.09640.09080.0569-0.02050.1084-0.04440.0472-2.41323.18491.353
104.55540.1373-0.32623.28631.37083.0753-0.0481-0.16620.5316-0.11170.03070.0961-0.4685-0.27660.01740.08670.0789-0.01280.1339-0.01460.0689-4.95323.98784.218
111.2818-1.6071-0.70662.58193.259810.6908-0.01510.06210.146-0.01530.0304-0.2113-0.07460.5584-0.01530.0678-0.01090.02120.1090.0540.1408-0.74511.988149.166
127.91344.88120.80586.4352-3.773414.14720.2922-0.0526-0.38630.3783-0.34340.0147-0.68470.64220.05120.0921-0.0646-0.01230.15310.0090.06414.37436.831144.057
130.8365-0.0639-0.22080.0936-0.07490.76450.09840.0370.0680.0181-0.05320.0125-0.1769-0.0444-0.04520.06950.01190.02240.0446-0.00030.0249-7.3541.925130.576
140.6968-0.3255-0.11960.75260.17970.4247-0.0105-0.0201-0.04770.0191-0.0061-0.01460.06150.03990.01660.04570.02140.01030.09170.00010.03760.94719.08124.231
151.68641.0101-0.12182.40230.18511.04690.02060.0491-0.0846-0.0089-0.035-0.0938-0.0150.08010.01440.04430.04780.01680.1135-0.00720.04996.20321.085117.102
160.87040.7148-0.07342.43520.48581.25480.01030.1301-0.0008-0.1484-0.03550.0389-0.05610.02810.02510.0690.04620.00330.13720.00420.06481.223.543114.67
170.65580.5980.11311.08220.15750.82270.05120.040.01370.0054-0.05610.0878-0.0204-0.04850.0050.04760.0381-0.0020.1001-0.00490.055-8.227.113121.837
182.10650.0745-0.08990.68960.03871.22920.07530.13250.0684-0.0478-0.0658-0.0797-0.15950.1449-0.00960.1095-0.010.01570.10190.02520.05257.91540.303122.099
197.6294-1.97480.18853.82991.76433.34120.1936-0.0044-0.84320.2632-0.1059-0.35590.13460.5409-0.08760.058-0.0268-0.06770.23260.06240.228723.67832.435134.333
203.21070.48951.21933.4459-0.20812.05180.13570.1369-0.24450.0283-0.084-0.43490.00450.4518-0.05170.0537-0.03870.01070.19090.01940.094522.64236.899128.947
214.2542-0.07590.24930.31671.773110.6527-0.12880.0353-0.05780.0890.0626-0.02420.49880.71860.06610.05660.0130.02080.22620.11370.142238.83176.65180.054
225.7182-2.088-0.68319.75260.526311.89180.04780.17850.1078-0.2066-0.0005-0.43720.38820.5629-0.04720.08640.07490.02410.13380.01030.023329.60348.57383.213
230.3576-0.31670.26480.5032-0.12840.7494-0.0074-0.0631-0.0374-0.02160.07750.05040.0688-0.1188-0.07010.0283-0.00990.00160.07470.02170.025511.18960.39296.543
241.0647-0.03010.44990.4635-0.13960.4356-0.01320.06930.05010.01680.0072-0.0509-0.00960.09380.00610.04360.0323-0.00590.0934-0.00730.039534.35867.904104.543
251.41470.35590.59881.2410.03881.1427-0.0286-0.08040.03230.08160.0407-0.03560.02730.0103-0.01220.04990.0473-0.00890.1169-0.00730.046433.08463.846111.885
262.6086-1.5902-0.589119.2097-1.31172.1939-0.0073-0.2066-0.13060.4645-0.03080.45680.0959-0.17780.03820.05820.02470.00190.1417-0.00070.021924.05564.386118.973
270.39820.49290.31621.43940.37580.8822-0.077-0.03310.0568-0.05630.10670.0602-0.0365-0.0423-0.02980.03690.03680.00440.104-0.00370.046721.15870.098103.889
281.2163-1.01130.3831.6982-0.37280.9113-0.0588-0.0908-0.1190.12640.09130.07610.135-0.0912-0.03240.0972-0.00340.00960.09720.02830.045115.04552.143104.909
291.47-0.2718-0.00873.39541.13992.59830.03250.0898-0.22140.02120.2659-0.50330.40610.3602-0.29830.09490.0759-0.03480.0909-0.07150.139935.64241.70898.771
302.87390.5367-0.15723.12071.67562.22810.05080.0513-0.22140.18680.2589-0.41830.3860.2958-0.30970.12890.0858-0.06470.0683-0.05080.088233.83540.41597.792
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 14
2X-RAY DIFFRACTION2A20 - 33
3X-RAY DIFFRACTION3A34 - 78
4X-RAY DIFFRACTION4A79 - 153
5X-RAY DIFFRACTION5A154 - 187
6X-RAY DIFFRACTION6A188 - 255
7X-RAY DIFFRACTION7A256 - 285
8X-RAY DIFFRACTION8A286 - 323
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